Wesker has Krauser work for Saddler as a double agent to gain his trust and eventually take a plaga sample. Saddler tasks Krauser to kidnap the US president's daughter Ashley Graham, which he successfully carries out. Krauser does not immediately retrieve the desired sample so Wesker sends Ada to infiltrate Saddler's territory and steal it.

Leon S. Kennedy, a now fully trained special agent working for the US Government, is sent out to rescue Ashley. Spanish cops act as Leon's backup and Ingrid Hannigan acts as Leon's contact to assist him throughout the mission.

Leon and Ada arrive in the village at the same time and are immediately attacked by the villagers. Ada manages to ring the Church bell to fend off the ganados for Leon. Ada finds out about the Los Iluminados and their ability to control las plagas. Leon meets Luis Sera and the two are captured and Leon is injected with a plaga sample.

They wake up later, break free and separate. Leon later runs into Bitores Mendez, but is aided by Ada Wong. Afterwards Ada is hit by a tranquilizing dart and is captured. Later, Leon passes out for six hours as the parasite inside him.

Leon regains consciousness and locates Ashley inside of a church. They run into Saddler but escape and head to a rendezvous point for a helicopter pickup.

Before reaching their destination, Hannigan informs them contact with the copter was lost. The two are ambushed by a horde of ganado and hide in a nearby house where Luis is also taking refuge in. Meanwhile, Ada awakens moments before a ganado attacks her and manages to find Luis just after Leon parted ways with him. Ada instructs Luis to give her a plaga sample as she knows he works for Saddler but, he had yet to retrieve a one.

Leon confronts Bitores Mendez and defeats him. Leon and Ashley are forced to take refuge in Salazar's nearby castle when a mob of ganado ambush them.

Leon and Ashley meet Ramon Salazar. Hannigan tries to contact Leon but the connection is cut off. Later, Ashley gets caught in a trap and is separated from Leon.

Along the way to find her, Leon has a formal confrontation with Ada. Leon knows of Ada's alliance with Wesker but she leaves before answering any of his questions.

Luis catches up to Leon to give him the plaga sample while Ada watches from a far. However, Saddler sneaks up behind Luis, kills him for betrayal, and takes back the sample. Leon then finds Ashley again and they set of to escape the castle.

Ashley is later captured by a Novistador and is brought to Salazar. Leon manages to catch up to the two but falls for a trap and gets separated.

Leon works his way back to the surface and to Salazar again. Salazar tells Leon that Ashley was taken to Saddler's island and then transforms into a monster which Leon defeats.

Leon finds Ada waiting for him in a small boat and together they head to the island. Meanwhile, Saddler orders Krauser to fetch Ashley and dispose of Leon.

Upon arriving, Ada goes her own way and Leon follows Ashley's trial. Leon frees Ashley from captivity and they try to escape.

They encounter Saddler again who controls and takes away Ashley, but Leon puts a tracking device on her. Meanwhile, Krauser and Ada discuss about the plaga sample and how Saddler has sniffed him out. Wesker order Krauser to kill Leon.

Ada acts on her own to try to find Leon to prevent his assassination. Along the way, she destroy Saddler's warship, which was going to use as plan B in case Ashley was rescued. Ada finally catches up to Krauser and rescues Leon before he is killed, Krauser retreats swearing Leon will die.

Still trying to locate Ashley, Krauser sets Leon on a goose chase to find keys as well as forcing Leon to fight him for one. Leon believes he defeats Krauser and moves on however, Krauser is only passed out and gravely wounded.

Mike arrives inside a helicopter to assist Leon reach Ashley. Mike is shot down and killed by a ganado with a RPG. Ada catches up with Leon, but Leon starts to be controlled by the plaga and attacks her. Ada is forced to defend herself and harms Leon which causes him to regain consciousness. The two go their own ways.

Ada is attacked by Krauser and defeats him once and for all but leaves his corpse as is.

Leon rescues Ashley who was in Saddler's chamber. Saddler tries to stop them, but Ada distracts and blocks his path so can't pursue the two. Ada engages Saddler but he knocks her out. Leon and Ashley find a machine that destroys the plaga in their bodies.

Leon finds Ada captive by Saddler and rescues her. Saddler transforms and engages in a fight with Leon. While the two fight, Ada makes her way around the scaffolding to retrieve a rocket launcher. She tosses it to Leon and he uses it to destroy Saddler. Ada leaves via helicopter having procured the plaga sample and gives Leon keys to a jet ski to escape the island while also initiating the island's self-destruct system. Leon and Ashley escape using the jet ski moments before self-destruction.

Hannigan reestablishes connection with Leon and he returns Ashley home to the president completing his mission. Leon later documents his experience in a file titled "The Kennedy Report". Ada sends an undesired sample to Wesker and sends the one from Saddler to her own employers she was actually working for the entire time. Wesker is forced to retrieve his own sample which he takes from Krauser's corpse.